Setting Things Right
by ShipperWriter
Summary: John takes a puddle jumper to say goodbye to an old friend. Episode tag for "Ghost in the Machine". Sparky angst.


**Author's Notes:** I had written this during Season 5 of SGA but never posted it here. Set just after "Ghost in the Machine".

**Disclaimer:** Don't own it, or else this episode never would have happened.

* * *

><p>He had stood on the steps in front of the Stargate, watched as a dark haired woman started to walk through, then as she turned to smile at him, he couldn't stand it anymore. He had to look away. If it was really her, she would understand. She knew him too well; she knew what he was feeling, even if he didn't.<p>

So with a smile on her face, she walked away. As the others followed her, John and his team knew that they would never see Elizabeth Weir again.

The wormhole disconnected, and John heard a voice confirm that the other terminal had indeed been a space 'Gate. That she was slowly shutting down, and if she remained undisturbed, would never be heard from again.

And John's heart broke for the third time in two years.

The first had been when the city was fleeing from the planet, when he had been in the chair, and in the midst of his celebratory cry, the first words he heard from Rodney McKay were, "We need a medical team to the control room, stat!"

And John ran through the city as fast as he could, and when he saw the unconscious woman laying on the stretcher, he nearly lost his voice as he asked, "Elizabeth . . . Is she gonna be okay?"

Less than 24 hours later, he had his answer. She would survive . . . due to the reactivated nanites in her body.

Not too soon after that was his second heartbreak. When he and Ronon had found her, standing in the corridor on Asuras with her hand inside of Oberoth's head, when the bugs started moving again, when he stubbornly wanted to refuse to leave her, when she shouted, "GO!" with all the power that she could muster from herself, when he told Samantha Carter that if she was still out there somewhere that he was going to find her . . . He never gave up on the idea that she was alive, but after a while he started to feel as if he wouldn't see her again.

Actually, his heart had broken four times. When she almost died. When he left her in the Replicator's hands. When her Repli-duplicate told him that the Asurans had killed her. And the last time, when he found out that she was truly alive, but to save the city she would sacrifice herself, just as she had done many times before.

And John couldn't take it anymore.

* * *

><p>One night, very soon after, John Sheppard snuck into the jumper bay, quietly fired up a jumper, and left the city, hoping that no one would notice him missing.<p>

He double-checked the coordinates. The ship helped him figure for interstellar drift and soon he found the 'Gate. As he approached, he noticed several white figures floating next to it. He moved the jumper in just enough to distinguish faces. As he found the one he wanted, his breath hitched in his throat. He couldn't let her go without setting things right.

He sealed the door leading to the back of the jumper and once it had closed tightly, he started to depressurize the back, and then he opened the ramp. He maneuvered the jumper so that one figure seemed to float into the back of the ship.

Once she was completely inside, he pulled the ramp back up and started to re-supply oxygen and air pressure to the room. When the HUD announced that it was balanced, he jumped up from his seat and hit the controls on the wall, opening the doors.

She lay on the floor, crystals right around her mouth from where she'd taken her last breath after she walked through the 'Gate. John stopped short; she vaguely looked like the Elizabeth Weir that he had known for three years and missed for two, with her hair being dark and that same determined expression that never seemed to leave her face.

He stifled a sob and knelt down next to her, touching her shoulder to rouse her. "Elizabeth? Hey, it's me, c'mon, open your eyes."

And her eyes opened suddenly, and she gasped, partly due to the change in environment and the figure who was kneeling next to her, hand firmly wrapped around her slender arm. "John," she breathed.

"Try to sit up," he told her, helping to move her.

She looked around and once she had her bearings, she whispered, "We're in a jumper?" looking to John for confirmation.

He nodded. "Yeah . . . It's just us."

She sighed at him. "How long since . . ."

"Three days," John informed her, his eyes never leaving her face as her own eyes darted around in slight confusion.

"Why did you come back?" she asked softly, looking down at the hard floor.

His hand lifted from her arm and, ever so slowly, reached up to touch her chin. "I never got a chance to say goodbye. Any of the times."

Her hurried face dropped to reveal a mask of caution and sympathy. His hand traveled to her cheek, his thumb running over it softly. "John . . ."

"Elizabeth, I know that you sacrificed yourself - twice now - to save the city and everyone in it. And I know that you, well, can't come home," he tried to explain, trying to convince himself at the same time. "But I - I couldn't let you go again without at least saying goodbye, without tellin' you the truth."

Her gaze looked up to meet his as his hand dropped away. "The truth?"

He smiled a little. "At least, to tell you one last time."

"Oh," she answered, realization washing over her as she fixed her view upon the windshield behind John. "So you're telling me that you stole a jumper in the middle of the night just to come out here and-"

"Tell you that I love you?" he finished for her, causing her to look up at him in shock. "Yes, that's exactly right. I guess you know me too well, 'Lizabeth," he grinned at her.

She smiled back. "I love you, John. I always have . . . And I always will, even if I'm not there."

"I know. I know you do," he replied, a solitary tear starting to make its way down his face. "God, Elizabeth - I miss you so much," he admitted quietly, his arms making their way around her chilled body.

She responded to him, wrapping her arms around his waist, holding onto him for dear life while she could, and she nestled her face into his neck. "I miss you too. But I saw how everything has been over the past few years."

"How?" he asked, pulling away slightly to look her in the face.

"While I was looking for a way out, I took a tour through the database. I saw all the mission reports, the personal logs - everything. That's how I found the design for this body in the system."

"Ah, makes sense."

"Without me, Atlantis hasn't fallen apart. It's gotten stronger, and you have yourselves to thank for that. Even if you spent every waking moment waiting for news about me, life went on. And, as much as I know you don't want to hear it, life will keep on going. Just look at Teyla. She had a baby! And everyone else has matured and stepped up, even if they didn't want to. Jennifer is one of the most skilled doctors in the universe now, after Carson died."

"Atlantis hasn't fallen apart," John conceded, "but that doesn't mean that I didn't."

"But you got back up, you didn't let it get the better of you. Just like you won't let this get you down after you leave here. I know you, John. I know you too well. I - I love you, and I will always."

John sighed, still trying to hold in the sorrow. He tipped her face upwards and softly kissed her lips. "I know you will."

The HUD crackled. "Jumper Four, this is Atlantis. Please respond."

"Crap," John muttered under his breath. He hadn't expected anyone to notice his disappearance that quickly, and even though all he wanted to do was just hold Elizabeth in his arms, he knew that their time was limited.

He released her from the embrace and touched his earpiece. "Sheppard here, go ahead, Rodney."

"John, thank God! We've been looking for you. Where are you?"

He advertently missed giving him a straight answer. "On my way back. Sheppard out."

As the comm crackled out, he turned back to Elizabeth. She had stood up, stretching. When she noticed the odd look from John, she wryly mentioned, "No matter what the Discovery Channel says, floating in space will cause stiffness."

John sighed, glancing between her and the front of the ship. "I guess I - it's time."

She only nodded, not wanting to betray the emotion on the verge of appearing. "Somehow, I doubt that this is the last time that you'll see me, John Sheppard."

"I hope so to God, Elizabeth Weir." He moved towards her and crushed her in his arms, lips colliding against hers one last time.

She pressed hers to his softly, one last time, and stared at him. "Remember what I said, John. Don't forget me . . . But don't dwell."

He nodded at her, kissing her forehead as they disentangled arms. "All right. I love you, Elizabeth."

She smiled. "I love you."

Leaving her standing there, he slowly backed up into the cockpit as the doors started to slide shut. His last glimpse of Elizabeth was a confident smile on her face, eyes closed as she prepared for her coma like state to take her again.

He depressurized the rear and opened the hatch, and slowly used the thrusters to move the jumper away.

* * *

><p>John arrived home on Atlantis, parked the jumper, avoided the questions from Rodney with the "I'm tired, I'll talk to you in the morning" brush-off and made it to his quarters without further annoyance.<p>

Making his way inside, he glanced around, seeing the pot that he had given to her their first year here, on her birthday. He smiled fondly at it, then stripped of his clothing and tangled himself under the sheets.

For the first time in years, he slept soundly through the night without the constant nightmare awakening him.

Waking up, his first thought was _Thank you, Elizabeth. Thank you for everything._

_I love you._

FIN


End file.
